Or, possibly, that each Virtual Console ROM ships with a set of shims or plugins to the emulator, to add extra logic and workarounds specific to each game.
Which is pretty much exactly how NES and SNES cartridges worked, come to think of it—except that the console they were patching was hardware, so they had to add new physical chips to do it. (Speaking of, I've always wondered why no console just ships with some FPGAs inside that are free for each game to program on startup.)
It'd be doable to have an FPGA there, it'd have to be an SRAM backed FPGA which will make it more expensive from what I've seen. Otherwise they're usually flash based which will wear out after a while. It'd also likely suffer a similar fate to the random processors in the playstation systems where they barely got any use in games to a serious extent since they were only on one system.
An fpga that would be useful is a relatively expensive piece of hardware, even at scale. Additionally, finding skilled professionals that would be able to work with them is much, much tougher than hiring a comparable graphics programmer.
There's also the issue of developing for an fpga being more difficult, and thus time consuming, than writing tight c.
Which is pretty much exactly how NES and SNES cartridges worked, come to think of it—except that the console they were patching was hardware, so they had to add new physical chips to do it. (Speaking of, I've always wondered why no console just ships with some FPGAs inside that are free for each game to program on startup.)